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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacagaattttccttggaactgtgtgacctttaatcaatctgcgtgagggcatggaacattttttttccctttcagtttacttaggcattttaaccttggtttcatcag

Basic information

species Zea mays
transcript GRMZM2G176903_T01
intron # 4
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71769569|gb|DR967506.1|DR967506
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|211251481|gb|FL481726.1|FL481726
EST:     TTTTTGGTGGAAGAGGAGTGACACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|76283460|gb|DV023028.1|DV023028
EST:     TTTTTGGTGGAAGAGGAGGGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|60394069|gb|DN226939.1|DN226939
EST:     TTTTTGGTGGAAGAGGAGTGACACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|91052484|gb|EB162902.1|EB162902
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATTTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|67012842|gb|CO441591.1|CO441591
EST:     TTTTTGGTGGAAGAGGAGTGACACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|93011745|gb|EB637265.1|EB637265
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|149075226|gb|EE163727.2|EE163727
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|148968047|gb|EE019380.2|EE019380
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAA
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAA
EST: gi|71449217|gb|DR830267.1|DR830267
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGC
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGC
EST: gi|61119403|gb|DN560364.1|DN560364
EST:     CAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: CAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|113844333|gb|DW954622.1|DW954622
EST:     CAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: CAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|44901166|gb|CK827711.1|CK827711
EST:     TTTTTGGTGGAAGAGGAGTGACACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|71763494|gb|DR961431.1|DR961431
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|71313076|gb|DR793065.1|DR793065
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|71305514|gb|DR788900.1|DR788900
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|71769570|gb|DR967507.1|DR967507
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTT
EST: gi|71313078|gb|DR793066.1|DR793066
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|91877438|gb|EB407395.1|EB407395
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|32834502|gb|CD974180.1|CD974180
EST:     TTTTTGGTGGAAGAGGAGTGACACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|93016813|gb|EB642333.1|EB642333
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
EST: gi|50324103|gb|CO519229.1|CO519229
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAG
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAG
EST: gi|211387055|gb|FL031624.1|FL031624
EST:     TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG                         CAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT
genomic: TTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 319

AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATTTACCTGAAAATAGAAGATTTGGCGAAGAAGTACCAGTGCAGCCCAGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATTTACCTGAAAATAGAAGATTTGGCGAAGAAGTACCAGTGCAGCCCAGCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 116

AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATTTACCTGAAAATAGAAGATTTGGCGAAGAAGTACCAGTGCAGCCCAGCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 273

AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacag ... gtttcatcagCAAAGGCATCCAAGATTTACAACAGAAAGCTTGGAGAAGAACAAGCAGATTTACCTGAAAATAGAAGATTTGGCGAAGAAGTACCAGTGCAGCCCAGCTC


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTGgtacgaacagaattttccttggaactgtgtgacctttaatcaatctgcgtgagggcatggaacattttttttccctttcagtttacttaggcattttaaccttggtttcatcag

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG